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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 12-79935553-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=79935553&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 10,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"gene_symbol": "PPP1R12A-AS1",
"hgnc_id": 51903,
"hgvs_c": "n.273A>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -10,
"transcript": "NR_146535.1",
"verdict": "Benign"
},
{
"benign_score": 10,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "PPP1R12A",
"hgnc_id": 7618,
"hgvs_c": "c.-221T>G",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -10,
"transcript": "NM_001143885.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_score": -10,
"allele_count_reference_population": 9012,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"chr": "12",
"clinvar_classification": "Benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6399999856948853,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3234,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000552885.2",
"gene_hgnc_id": 51903,
"gene_symbol": "PPP1R12A-AS1",
"hgvs_c": "n.653A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000552885.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1403,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000798430.1",
"gene_hgnc_id": 51903,
"gene_symbol": "PPP1R12A-AS1",
"hgvs_c": "n.245A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000798430.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 495,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000798431.1",
"gene_hgnc_id": 51903,
"gene_symbol": "PPP1R12A-AS1",
"hgvs_c": "n.307A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000798431.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1621,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000798432.1",
"gene_hgnc_id": 51903,
"gene_symbol": "PPP1R12A-AS1",
"hgvs_c": "n.205A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000798432.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1537,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NR_146533.1",
"gene_hgnc_id": 51903,
"gene_symbol": "PPP1R12A-AS1",
"hgvs_c": "n.273A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_146533.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1412,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NR_146534.1",
"gene_hgnc_id": 51903,
"gene_symbol": "PPP1R12A-AS1",
"hgvs_c": "n.273A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_146534.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1308,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NR_146535.1",
"gene_hgnc_id": 51903,
"gene_symbol": "PPP1R12A-AS1",
"hgvs_c": "n.273A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_146535.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 995,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4639,
"cdna_start": null,
"cds_end": null,
"cds_length": 2988,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000437004.6",
"gene_hgnc_id": 7618,
"gene_symbol": "PPP1R12A",
"hgvs_c": "c.-221T>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000416769.2",
"strand": true,
"transcript": "ENST00000437004.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1030,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5582,
"cdna_start": null,
"cds_end": null,
"cds_length": 3093,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001143885.2",
"gene_hgnc_id": 7618,
"gene_symbol": "PPP1R12A",
"hgvs_c": "c.-221T>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001137357.1",
"strand": true,
"transcript": "NM_001143885.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1030,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5582,
"cdna_start": null,
"cds_end": null,
"cds_length": 3093,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000261207.9",
"gene_hgnc_id": 7618,
"gene_symbol": "PPP1R12A",
"hgvs_c": "c.-221T>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000261207.5",
"strand": true,
"transcript": "ENST00000261207.9",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 995,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5477,
"cdna_start": null,
"cds_end": null,
"cds_length": 2988,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001244990.2",
"gene_hgnc_id": 7618,
"gene_symbol": "PPP1R12A",
"hgvs_c": "c.-221T>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001231919.1",
"strand": true,
"transcript": "NM_001244990.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs76824425",
"effect": "splice_region_variant,non_coding_transcript_exon_variant",
"frequency_reference_population": 0.009142203,
"gene_hgnc_id": 51903,
"gene_symbol": "PPP1R12A-AS1",
"gnomad_exomes_ac": 7467,
"gnomad_exomes_af": 0.00895876,
"gnomad_exomes_homalt": 31,
"gnomad_genomes_ac": 1545,
"gnomad_genomes_af": 0.0101463,
"gnomad_genomes_homalt": 25,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 56,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.106,
"pos": 79935553,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NR_146535.1"
}
]
}